Novel regulatory t cell epitope and hepatitis c virus homolog

ABSTRACT

A pharmaceutical composition used to suppress immunity in an animal, wherein the pharmaceutical composition comprises an isolated T-cell epitope peptide containing an amino acid sequence of PLLLLL L XLPXRA (SEQ ID NO: 5), wherein X is an amino acid.

CROSS REFERENCE TO RELATED APPLICATION

This application claims priority from U.S. Provisional Application Ser. No. 61/899,617 filed Nov. 4, 2013, the entire content and substance of which is incorporated by reference herein in its entirety.

SUPPORT

This invention was made with government support under (Grant No. U19 AI082642 awarded by National Institutes of Health Research. The government has certain rights in the invention.

BACKGROUND

Artificial induction of tolerance to self or to foreign antigens is the goal of therapy for autoimmunity, transplantation allergy and other diseases, and is also desirable in the context of therapy with autologous proteins and non-autologous proteins. Until recently, therapeutic tolerance induction relied on broad-based approaches that resulted in cellular depletion and cytokine profile alteration. These broad-based approaches weaken the immune system in general and leave many subjects vulnerable to opportunistic infections, autoimmune attack and cancer. There is a need in the art for less aggressive and more targeted approaches to the induction of immune tolerance.

Immune tolerance is regulated by a complex interplay between T cells, B cells, cytokines and surface receptors. Initial self/non-self discrimination occurs in the thymus during neonatal development where medullary epithelial cells express specific self protein epitopes to immature T cells. T cells recognizing self antigens with high affinity are deleted, but autoreactive T cells with moderate affinity sometimes avoid deletion and can be converted to so called ‘natural’ regulatory T cells (T_(reg)) cells. These natural T_(reg) cells are exported to the periphery and provide for constant suppression of autoimmunity.

A second form of tolerance occurs in the periphery where mature T cells are converted to an ‘adaptive’ T_(reg) phenotype upon activation via their T cell receptor in the presence of IL-10 and TGF-.beta. The possible roles for these ‘adaptive’ T_(reg) cells include dampening immune response following the successful clearance of an invading pathogen as a means of controlling excessive inflammation as might be caused by an allergic reaction or low level chronic infection, or possibly to facilitate co-existence with beneficial symbiotic bacteria and viruses. ‘Adaptive’ T_(reg) may also play a role in managing the life cycle of human antibodies that have undergone somatic hypermutation.

Natural regulatory T cells are a critical component of immune regulation in the periphery. Upon activation through their TCR natural Tregs are capable of suppressing bystander effector T cell responses to unrelated antigens through contact dependent and independent mechanisms. In addition the cytokines released by these cells including IL-10 and TGF-.beta., are capable of inducing antigen-specific adaptive Tregs. Despite extensive efforts, with few exceptions, the antigen specificity of natural Tregs, and more importantly natural T_(reg) circulating in clinically significant volumes, is still unknown.

There is need in the art for the identification of new regulatory T cell epitopes contained in common autologous proteins such as IgG (“Tregitopes”) and for methods for related to their preparation and of use.

Chronic hepatitis C virus (HCV) infection is a major public health concern worldwide. It is the leading cause of liver failure and reason for liver transplant in the US. Irrespective of clinical outcome, acute HCV infections are characterized by broad HCV-specific T cell responses that correlate with spontaneous viral clearance in a minority of individuals. In most patients, however, this initial response fails to contain the virus and chronic disease results. Increased numbers of CD4⁺ regulatory T_((reg)) cells circulating in the bloodstream and accumulating in the liver have been implicated in the pathogenesis of chronic hepatitis C.

T_(reg) cells constitute one of the major mechanisms underlying immunological homeostasis and self-tolerance. In addition, T_(reg) cells play a key role in moderating the immune response to infectious diseases, suppressing host tissue and organ damage that would occur in the absence of regulation. Although key to maintaining immune homeostasis, a growing body of evidence suggests that T_(reg) cells also contribute to the establishment and persistence of chronic infections, e.g., HCV. While no single marker exists, human T_(reg) cells are classically identified by expression of the transcription factor, forkhead box P3 (FoxP3), and the cell surface expression of the interleukin (IL)-2 receptor a chain (CD25). Bystander suppression is an additional key feature of T_(reg) cells.

Two distinct T_(reg) cell subsets are described in the literature: natural (n)T_(reg) cells specific for self epitopes and generated by high-avidity selection in the thymus, and inducible (i)T_(reg) cells that derive from conventional (CD4⁺CD25⁻FoxP3⁻) T cells following stimulation in the periphery. nT_(reg) cells can induce the conversion of conventional T cells to iT_(reg) cells via cytokine-dependent and -independent mechanisms, a process called infectious tolerance. Notably, the factors that affect expansion of the T_(reg) cell population in cases of chronic hepatitis C remain to be fully delineated. Nonetheless, the consensus supports the heterogeneous nature of the expanded T_(reg) cell population composed of both nT_(reg) and iT_(reg) cell subsets.

BRIEF DESCRIPTION OF DRAWINGS

FIG 1: HCV_G1_p7_(—)794 induces the production of CD3⁺CD4⁺FoxP3⁺ cells in cultures of PBMCs derived from HCV-infected patients.

FIG. 2: HCV_G1_p7_(—)794 fails to elicit a significant increase in CD3⁺CD4⁺FoxP3⁺ cells in PBMC cultures derived from non-infected individuals or patients who spontaneously cleared infection.

FIG. 3: CD3⁺CD4⁺FoxP3⁺ T cells do not proliferate in response to HCV_G1_p7_(—)794.

FIG. 4: Human p7_(—)794 analog stimulates a significant increase in CD3⁺CD4⁺FoxP3⁺ T cells in HCV-infected and non-infected individuals.

FIG. 5: Fewer HCV-G1_p7_(—)794-responsive T_(reg) cells express CD304 (neuropilin).

SUMMARY OF THE INVENTION

The present invention harnesses the functions of regulatory T cells (T_(reg)), particularly those cells that already regulate immune responses to foreign and self proteins in the periphery (pre-existing or natural T_(reg)). In one aspect, the invention provides T-cell epitope polypeptide compositions.

The selective engagement and activation of pre-existing natural Treg through the use of Tregitopes and Tregitope-antigen fusions, is therapeutically valuable as a means of treatment for any disease or condition marked by the presence of an unwanted immune response created by autoimmune diseases, such as, but not limited to, Crohn's Disease, Guillian Barre Syndrome, Lupus, Psoriasis, Rheumatoid Arthritis, Ulcerative Colitis and Multiple Sclerosis; pre- or post-transplanations; allergies such as, but not limited to, asthma, COPD and allergic rhinitis. The present invention is directed to the use of a peptide in the HCV p7 protein, HCV_G1_p7_(—)794 (SEQ ID NO: 1), residing in the hepatitis C virus (HCV), for the control of unwanted immune response. A further embodiment is the human analog (SEQ ID NO: 2) of the HCV_G1_p7_(—)794, H p7_(—)794.

In one embodiment, the present invention is directed to a T-cell epitope polypeptide composition comprising at least one polypeptide selected from the group consisting of: SEQ ID NOS: 1 and 2. In a particular embodiment, the invention is directed to a pharmaceutical composition comprising a polypeptide of the invention and a pharmaceutically acceptable carrier.

In a second embodiment, the present invention is directed to a nucleic acid encoding at least one T-cell epitope polypeptide selected from the group consisting of: SEQ ID NOS: 1 and 2. In a particular embodiment, the invention is directed to a vector comprising a nucleic acid of the invention. In yet another embodiment, the invention is directed to a cell comprising a vector of the invention.

In a third embodiment, the invention is directed to a method of treating or preventing a medical condition in a subject in need thereof comprising administering a therapeutically effective amount of a T-cell epitope polypeptide selected from the group consisting of: SEQ ID NOS: 1 and 2. In a particular embodiment, the medical condition is selected from the group consisting of: an allergy, an autoimmune disease, a transplant related disorder, graft versus host disease, an enzyme or protein deficiency disorder, a hemostatic disorder, cancer, infertility; and a viral, bacterial or parasitic infection.

In fourth embodiment, the present invention is directed to a method for repressing immune response in a subject, comprising administering a composition comprising a therapeutically effective amount of a peptide comprising SEQ ID NOS: 1 or 2 to the subject, wherein the peptide represses the immune response. In a particular embodiment, the peptide suppresses effector T cell response. In a particular embodiment, the peptide suppresses helper T cell response. In another embodiment, the peptide suppresses B cell response.

In a fifth embodiment, the present invention is directed to a method of suppressing antigen specific immune response in a subject through the administration of a therapeutically effective amount of a composition comprising SEQ ID NOS: 1 or 2, wherein the one or more Tregitopes are either covalently bound, non-covalently bound or in admixture with a specific target antigen resulting in the diminution of immune response against the target antigen. In a particular embodiment, the suppressive effect is mediated by natural Treg. In another embodiment, the suppressive effect is mediated by viral homolog of the natural Treg. In another embodiment, the peptide suppresses effector T cell response. In another embodiment, the peptide suppresses helper T cell response. In another embodiment, the peptide suppresses B cell response.

In a sixth embodiment, the present invention is directed to a method for enhancing the immunogenicity of a vaccine delivery vector, comprising identification and removal of regulatory T cell epitopes residing in the vaccine to hepatitis C virus. In a particular embodiment, the T cell epitopes are selected from the group consisting of: SEQ ID NOS: 1 or 2. In a further embodiment, a vaccine delivery vector with removed regulatory T cell epitopes is further enhanced, comprising (a) isolating regulatory T-cells from the biological sample; (b) contacting the isolated regulatory T-cells with an effective amount of a Tregitope composition of the enhanced vaccine delivery vector; (c) identification of the sequences; and (d) removal of remaining regulatory T cell epitopes residing in the vaccine.

In a seventh embodiment, the present invention is directed to a method to reduce the repressing immune response in a subject infected with the hepatitis C virus, comprising administering a therapeutically effective of the antibody recognizing a peptide from the group consisting of: SEQ ID NOS: 1 and 2.

DETAILED DESCRIPTION OF INVENTION

Spontaneous resolution of hepatitis C virus (HCV) infections depends upon a broad T cell response to multiple viral epitopes. Most patients fail to clear infections spontaneously, however, and develop chronic disease. The elevated number and function of CD3⁺CD4⁺CD25⁺FoxP3⁺ regulatory T_((reg)) cells in HCV-infected patients suggest the role of T_(reg) cells in impaired viral clearance. Factors contributing to increased T_(reg) cell activity in chronic hepatitis C cases remain to be delineated.

Resolution of primary HCV infections is dependent upon the vigorous response of CD4⁺ and CD8⁺ T cells to multiple viral epitopes. HCV persists in the majority of infected patients, however, by modifying and/or evading the host immune response. Purportedly, a variety of factors contribute to the diminished T cell responses observed in chronically infected patients including: viral mutation and escape linked to both CD4 and CD8 T cell failure, CD4 T cell anergy, CD8 T cell exhaustion, impaired dendritic cell function, and T_(reg) cell-mediated suppression. The increased frequency of T_(reg) cells found in the liver and circulating in the peripheral blood of chronically-infected patients provided an initial indication of the role of T_(reg) cells in the pathogenesis of chronic hepatitis C. It remained unclear until recently, however, whether this increase represented the HCV epitope-specific response of T_(reg) cells or the nonspecific consequence of chronic inflammation and liver disease.

Immunoinformatics tools were used to predict promiscuous, highly-conserved HLA-DRB1-restricted immunogenic consensus sequences (ICS), each composed of 5-6 T cell epitopes. These sequences were synthesized and added to cultures of peripheral blood mononuclear cells (PBMCs) derived from patients who resolved HCV infection spontaneously, patients with persistent infection, and non-infected individuals.

In the present invention, surprisingly a unique viral peptide derived from HCV p7 protein (HCV_G1_p7_(—)794) was identified that promotes a T_(reg) cell response among PBMCs derived from patients with persistent HCV infection. This peptide exhibited human homology when evaluated using GenBank Basic Local Alignment Search Tool (BLAST). Further analysis using a new bioinformatics tool, JanusMatrix, demonstrated that this HCV peptide cross-reacts with HLA matched peptide sequences located within hundreds of human proteins. Our invention showed that HCV_G1_p7_(—)794 engages preexisting nT_(reg) cells, as a consequence of this homology, induces infectious tolerance and the expansion an iT_(reg) cell population, which contributes to suppression of effector T_((eff)) cell activity in cases of chronic HCV infection. Further, a virus-encoded peptide (HCV_G1_p7_(—)794) with extensive human homology activates cross-reactive CD3⁺CD4⁺CD25⁺FoxP3⁺ nT_(reg) cells, contributing to immunosuppression and chronic hepatitis C.

The invention provides methods of treating a subject with a medical condition comprising administering a therapeutically effective amount of a T cell epitope selected from the group consisting of: SEQ ID NOS: 1 or 2 in a pharmaceutically acceptable carrier or excipient. The T cell epitope of the present invention can be incorporated into pharmaceutical compositions suitable for administration. The pharmaceutical compositions generally comprise at least one T cell epitope and a pharmaceutically-acceptable carrier in a form suitable for administration to a subject. Pharmaceutically-acceptable carriers are determined in part by the particular composition being administered, as well as by the particular method used to administer the composition.

EXAMPLE 1 A Peptide Sequence in HCV p7 Exhibits Human Homology

Sustained, virus-specific CD4 and CD8 T cell responses are associated with successful control of HCV infection. Therapeutic vaccination offers a rational approach to stimulating host resistance and overcoming viral persistent in cases of chronic disease. Toward this end, 20 promiscuous HCV (genotype 1) ICS were predicted and validated by demonstrating their ability to bind a panel of the eight common alleles HLA-DRB1 alleles: DRB1*0101, *0301, *0401, *0701, *0801, *1101, *1301, and *1501, representing essentially the entire human population. One ICS, located within HCV p7 protein (HCV_G1_p7_(—)794; WPLLLLLLALPQRAYAQ), exhibited significant human homology (>70% shared identities) determined by GenBank BLAST analysis; none of the remaining ICS exhibited the same homology.

HCV sequences were acquired from the Los Alamos sequence and immunology database. Nine-mer amino acid sequences, capable of fitting the binding groove of HLA class II molecules and highly conserved across HCV genotype 1a and 1b isolates, were identified using bioinformatics tools. Each 9-mer was scored for its predicted potential to bind a panel of eight HLA class II alleles (DRB1*0101, DRB1*0301, DRB1*0401, DRB1*0701, DRB1*0801, DRB1*1101, DRB1*1301 and DRB1*1501).

HLA class II immunogenic consensus sequences (ICS) were constructed by assembling potentially immunogenic 9-mers into 18-25 amino acid sequences. ICS construction improves the probability that an epitope will be presented in the context of more than one HLA allele, thus broadening the response of an HLA-diverse human population. Twenty ICS were synthesized as peptides using 9-fluoronylmethoxycarbonyl chemistry and purified >85% by 21st Century Biochemicals (Marlboro, Mass.). As predicted, each of these “promiscuous” ICS was bound by multiple HLA-DRB1 alleles in competitive binding assays performed in accordance with methods we described previously. Each ICS was also evaluated for human homology (>7 shared identities per 9-mer frame) using GenBank BLAST.

EXAMPLE 2 HCV_G1_p7_(—)794 Induces a CD3⁺CD4⁺FoxP3⁺ T Cell Response in HCV-Infected Patients

HCV-seropositive subjects with persistent viremia (Ab⁺VL⁺), patients who spontaneously resolved infection (Ab⁺VL⁻) and HCV-seronegative, non-infected (Ab⁻VL⁻) individuals were recruited from the Rhode Island Adult Corrections Institution (ACI) to participate in this study. Recruitment methods and the population are described elsewhere. The Institutional Review Boards of the Miriam Hospital, Rhode Island Department of Corrections and Office of Human Research Protection approved this study. All HCV infected subjects included in these analyses were infected with HCV genotype 1a or 1b (Versant HCV genotype assay 2, Siemens Healthcare Diagnostics Inc.). Hartford Hospital Transplantation Research Laboratory (Hartford, Conn.) and the Cellular Mediated Immunology Core Laboratory at the University of Rhode Island (Providence, R.I.) performed HLA typing. Subject demographic and serologic data are shown in Table 1.

TABLE 1 Viral Load Geno- Anti- ID# Age HCV Status IU/ml type body HLA-DRB1 229 28 Infected 170,620 1 + 03,11 236 29 Infected 602,611 1 + 01,11 261 25 Infected 7,464,611 1 + 01,11 265 22 Infected 21,917,190  1a + 13,15 272 23 Infected 458  1a + 03,11 279 25 Infected 1,788,326  1a + 13,15 282 28 Infected 186,678  1a + 03,04 216 23 Clearer NA NA + 07:01 221 27 Clearer NA NA + 03,11 222 25 Clearer NA NA + 03,15 246 26 Clearer NA NA + 01,04 267 23 Clearer NA NA + 03,11 264 27 Clearer NA NA + 03,11 248 26 Non-infected NA NA − 04,11 259 26 Non-infected NA NA − 04,11 262 22 Non-infected NA NA − 03,11 257 22 Non-infected NA NA − 03,15 263 26 Non-infected NA NA − 01,03 268 21 Non-infected NA NA −

A series of experiments was undertaken to determine and compare the HCV_G1_p7_(—)794-specific responses of PBMCs obtained from non-infected control individuals (Ab⁻VL⁻), patients who spontaneously cleared HCV infection (Ab⁺VL⁻) and infected patients in whom viremia persisted (Ab⁺VL^(⇄)).

Cryopreserved PBMCs were thawed; suspended in HEPES-buffered RPMI1640 medium supplemented with 10% HuAB serum (Valley Biomedical, Winchester, Va.), glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin; and rested overnight at 37° C. in a humidified, CO₂ incubator. On the following day, the PBMCs were centrifuged and resuspended in fresh medium containing 5% HuAB serum; 1×10⁶ cells/nil were transferred to deep, flat-bottom, non-treated 48-well plates. The peptide sequence indicated in the text was added (10 μg/ml final concentration) and the cells were incubated for 5 days. PBMCs cultured in the presence of medium with 0.1% DMSO served as a negative control. Half the spent medium was replaced on day 3. The cells were collected for analysis on day 5.

For proliferation assays, cells rested overnight were labeled with carboxyfluorescein diacetate, succinimidyl ester (CFSE: Life Technologies Corporation, Carlsbad, Calif.) prior to culture in the presence or absence of 30 ng/ml anti-CD3 monoclonal antibody (clone HIT3a; BioLegend, San Diego, Calif.) and 10 μg/ml HCV_G1_p7_(—)794. Cell proliferation was evaluated by flow cytometric analysis according to the protocol provided by Life Technologies in which a loss in fluorescence intensity correlates directly with the extent of replication.

The cells collected after 5 days incubation were quantified and characterized in accordance with methods we described previously. Dye-conjugated mouse monoclonal antibodies specific for the following determinants were purchased from BioLegend (San Diego, Calif.) and used: CD3, CD4 (clone OKT4), CD8a (clone HIT8a); CD39 (clone A1), and CD304 (clone 14H4); anti-human CD25 (clone M-A251) and anti-human FoxP3 (clone 236a) were purchased BD Biosciences (San Jose, Calif.). Data were collected on a 4 laser (13 color capability) BD LSRII Flow Cytometer (BD Biosciences, San Jose, Calif.) and analyzed using FlowJo software (Tree Star, Inc., Ashland, Oreg.). All analyses were conducted using the appropriate isotype controls to correct for non-specific staining PBMCs were cultured in the presence of medium alone, 10 μg/ml HCV_G1_p7_(—)794, or 10 μg/ml HCV_G1_NS4b_(—)1941.

The results were analyzed using the SigmaStat statistics program (Aspire Software International). Individual means were compared using a non-paired Student's t test or a Mann-Whitney Rank Sum test. Data derived from 3 or more groups were compared by one-way analysis of variance; the Dunnett's test was used to determine which groups differed significantly.

The cells were collected after 5 days incubation and analyzed by flow cytometry (FIG. 1A). The CD3⁺CD4⁺FoxP3⁺ cells were further characterized by the expression of CD25 and CD39 (FIG. 1B). The gating scheme and representative analyses are shown.

HCV_G1_p7_(—)794 induced a marked increase in CD3⁺CD4⁺FoxP3⁺ cells when added to PBMC cultures derived from infected, Ab⁺VL⁺ patients (FIG. 1A). In contrast, HCV_NS4B_(—)1941 (AARVTQILSSLTITQLLKRLHQWT; an ICS that exhibits little human homology) failed to promote an increase in CD3⁺CD4⁺FoxP3⁺ cells when added to PBMC cultures derived from Ab⁺VL⁺ individuals. Other highly conserved HCV ICS with negligible human homology (e.g., HCV_G1_NS4b_(—)1769; ISGIQYLAGLSTLPGNPA) similarly failed to elicit a CD3⁺CD4⁺FoxP3⁺ cell response (data not shown). The CD3⁺CD4⁺FoxP3⁺ cells induced by the addition of HCV_G1_p7_(—)794 to Ab⁺VL⁺ PBMC cultures expressed both CD25 (IL-2 receptor a chain, constituently expressed by T_(reg) cells) and CD39, a cell ectonucleotidase associated with T_(reg) cell suppressor function (FIG. 1B).

Ab⁺VL⁺ patients also had a higher baseline level of CD3⁺CD4⁺Foxp3⁺ cells compared to spontaneously clearers and non-infected controls, a finding consistent with the literature (FIG. 2). PBMCs obtained from infected patients (Ab⁺VL⁺, n=4), patients who clear infection (Ab⁺VL⁻, n=6) and non-infected controls (Ab⁻VL⁻, n=4) were cultured in the presence of medium alone, 10 μg/ml HCV_G1_p7_(—)794 or 10 μg/ml HCV_G1_NS4b_(—)1941. The cells were collected after 5 days incubation, stained and analyzed by flow cytometry as outlined schematically in FIG. 1; *Significantly different, P=0.014; **significantly greater than all other groups, P<0.001.

Further, neither HCV_G1_p7_(—)794 (putative Treg epitope) nor HCV_G1_NSB4_(—)1941 (putative T effector epitope) added to PBMC cultures derived from non-infected individuals or from patients who successfully cleared HCV infection induced a significant increase in CD3⁺CD4⁺FoxP3⁺ cells.

EXAMPLE 3 HCV_G1_p7_(—)794 Induces an Increase in CD3⁺CD4⁺FoxP3⁺ T Cells in the Absence of Proliferation

The hallmark of CD3⁺CD4⁺FoxP3⁺ T_(reg) cells is suppressor activity. CSFE-labeled, Ab⁺VL⁺ PBMCs were cultured with medium alone or medium that contained 30 ng/ml anti-CD3, 10 μg/ml HCV_G1_p7_(—)794 or a combination of anti-CD3 and HCV_G1_p7_(—)794. After 5 days incubation, the cells were collected and proliferation the total (FIG. 3BA) and CD3⁺CD4⁺ (FIG. 3B) PBMC populations was estimated by flow cytometry. Data were obtained in a single experiment representative of the results obtained for PBMCs derived from six HCV-infected patients.

CD3⁺CD4⁺FoxP3⁺ T cells do not proliferate in response to HCV_G1_p7_(—)794. PBMCs obtained from HCV-infected patients (Ab⁺VL⁺, n=4) and non-infected controls (Ab⁻VL⁻, n=4) were cultured in the presence or absence of 10 μg/ml of human p7_(—)794 analog. The cells were collected after 5 days incubation and analyzed by flow. Significantly more CD3⁺CD4⁺FoxP3⁺ cells were recovered from PBMC cultured with the human p7_(—)794 analog than medium alone: *P=0.001; **P=0.048.

The addition of HCV_G1_p7_(—)794 to Ab⁺VL⁺ PBMC cultures resulted in a reproducible, albeit slight, decrease in the proliferative response to anti-CD3 monoclonal antibody treatment whether the total (FIG. 3A) or CD3⁺CD4⁺ (FIG. 3B) cell population was assessed. Importantly, the addition of HCV_G1_p7_(—)794 alone (i.e., in the absence of anti-CD3) had no effect on the proliferation of CD3⁺CD4⁺ T cells obtained from the same patient population. This finding suggests that HCV_G1_p7_(—)794 induces the conversion of conventional CD3⁺CD4⁺FoxP3⁻ T cells to CD3⁺CD4⁺FoxP3⁺ iT_(reg) cells, rather than stimulating the proliferation of T_(reg) cells already present.

EXAMPLE 4 HCV_G1_p7_(—)794 Activates Cross-Reactive nT_(reg) Cells and Induces Infectious Tolerance

A human analog of HCV_G1_p7_(—)794 (p7_(—)794, PLLLLLLSLPPRA) was identified by GenBank BLAST analysis and synthesized in an effort to provide a clearer understanding of the nature of the T_(reg) cells that respond to HCV_G1_p7_(—)794. Like the HCV-encoded homolog, the human analog induced a significant increase in CD3⁺CD4⁺FoxP3⁺ cells in PBMC cultures derived from patients with persistent viremia (FIG. 4).

Human p7_(—)794 analog stimulated a significant increase in CD3⁺CD4⁺FoxP3⁺ T cells in HCV-infected and non-infected individuals. PBMCs obtained from HCV-infected patients (Ab⁺VL⁺, n=4) and non-infected controls (Ab⁻VL⁻, n=4) were cultured in the presence or absence of 10 μg/ml of human p7_(—)794 analog. The cells were collected after 5 days incubation and analyzed by flow. Significantly more CD3⁺CD4⁺FoxP3⁺ cells were recovered from PBMC cultured with the human p7_(—)794 analog than medium alone: *P=0.001; **P=0.048.

In contrast to HCV_G1_p7_(—)794, the human analog also induced an approximate three-fold increase in CD3⁺CD4⁺FoxP3⁺ cells in PBMC cultures derived from non-infected individuals indicating the response of an nT_(reg) cell population.

CD304 (neuropilin-1) is expressed by a subset of FoxP3⁺ T_(reg) cells in humans. In mice, CD304 expression differentiates natural (CD304⁺), from inducible (CD304⁻), T_(reg) cells. PBMCs obtained from an infected patient (representative of 4 patients) were incubated in medium alone (A) or medium that contained 10 μg/ml HCV_G1_p7_(—)794 (B). The cells were collected on day 5, stained and analyzed by flow. Panels on the right indicate the percentage of CD4⁺FoxP3⁺ cells in each population that expresses CD304. While a similar distinction has yet to be reported in humans, it is pertinent to note that the bulk of CD4⁺FoxP3⁺ cells contained among Ab⁺VL⁺ PBMCs cultured in the absence of HCV_G1_p7_(—)794 expressed CD304 indicative of nT_(reg) cells (FIG. 5A). In contrast, the vast majority of CD4⁺FoxP3⁺ cells among Ab⁺VL⁺ PBMCs cultured in the presence of HCV_G1_p7_(—)794 were CD304-negative characteristic of iT_(reg) cells (FIG. 5B). Together these findings showed that HCV_G1_p7_(—)794 recognition by nT_(reg) cells following HCV exposure promotes infectious tolerance and the production of FoxP3⁺ iT_(reg) cells from conventional CD4⁺FoxP3⁻ T_(eff) cells.

EXAMPLE 5 JanusMatrix Confirms T_(reg) Cell Epitopes Shared by HCV_G1_p7_(—)974 and the Human Proteome

By comparing HCV G1_p7_(—)794 with peptide sequences found within the human proteome, JanusMatrix analysis provided further insight into the capacity of HCV_G1_p7_(—)794 to induce a T_(reg) cell response by PBMCs derived from HCV-infected patients.

Crystal structure analyses of ternary, MHC:epitope: T cell receptor (TcR) complexes indicate that certain amino acid residues of a T cell epitope contact the MHC molecule while other residues contact the TcR. The TcR contacts can be modeled using a new bioinformatics tool, JanusMatrix. This tool interrogates potential T cell epitopes from both its HLA-binding and TcR-facing aspects, and assesses TcR cross-reactivity with T cell epitopes that are present in the human genome and in the human microbiome, or other genomes. Those epitopes from two different genomic sources, e.g., HCV and human, that bind the same HLA molecules and present identical amino acids to the TcR are designated potentially cross-reactive, as they may stimulate the same TcR and trigger the same T cell to respond. In the analysis, JanusMatrix divided the HCV HLA-DRB1-restricted epitopes (comprising the ICS described above) into TcR-facing and MHC-binding amino acid residues. The human protein database (UniProtKB) was searched for TcR-facing epitopes that cross-react with epitopes encoded by HCV.

As illustrated in Table 2, HCV_G1_p7_(—)794 consists of 6 T cell epitopes, 5 of which cross-react with 152 putative human T cell epitopes contained in 264 different human proteins. Similarly, the human analog, p7_(—)794, cross-reacts with putative T cell epitopes located within several hundred human proteins. On the other hand, neither HCV_G1_NS4b_(—)1941 (control ICS often used in the ex vivo experiments described above) nor any of the other 18 ICS, which were originally predicted and validated (data not shown), exhibited significant cross-reactivity with the human proteome. The results of these analyses support the speculation that HCV_G1_p7_(—)794 activates a cross-reactive nT_(reg) cell population that normally functions to suppress autoimmune responses to a large number of human proteins, which contain a common peptide sequence (epitope).

TABLE 2 Comparison of Peptide Sequences # Cross-Reactive Epitopes per in Human Description ICS Sequence ICS Proteins HCV_G1_p7_794 WPLLLLLLALPQ 5.0 264 RAYAQ SEQ ID NO: 1 Human p7_794 PLLLLLLSLPPR 4.0 325 A SEQ ID NO: 2 HCV_G1_NS4b_1941 AARVTQILSSLT 6.0  28 ITQLLKRLHQWI

The present invention demonstrated that ICS, HCV_G1_p7_(—)794, induced a marked increase in T_(reg) cells in PBMC cultures derived from infected patients, but not those patients who spontaneously cleared HCV or non-infected individuals. An analogous human peptide (p7_(—)794), on the other hand, induced a significant increase in T_(reg) cells among PBMCs derived from both HCV infected and non-infected individuals. JanusMatrix analyses determined that HCV_G1_p7_(—)794 is comprised of T_(reg) cell epitopes that exhibit extensive cross-reactivity with the human proteome.

This unique viral peptide derived from HCV p7 protein (HCV_G1_p7_(—)794) promoted a T_(reg) cell response among PBMCs derived from patients with persistent HCV infection. It also exhibited human homology when evaluated using GenBank Basic Local Alignment Search Tool (BLAST). Further analysis using a new bioinformatics tool, JanusMatrix, demonstrated that this HCV peptide cross-reacts with HLA matched peptide sequences located within hundreds of human proteins. The data demonstrated that HCV_G1_p7_(—)794 engaged preexisting nT_(reg) cells, as a consequence of this homology, induces infectious tolerance and the expansion an iT_(reg) cell population, which contributes to suppression of effector T_((eff)) cell activity in cases of chronic HCV infection. It is concluded that HCV_G1_p7_(—)794 with extensive human homology activates cross-reactive CD3⁺CD4⁺CD25⁺FoxP3⁺ nT_(reg) cells, contributing potentially to immunosuppression and chronic hepatitis C.

The ability of HCV-derived epitopes to stimulate T_(reg) cell responses is well documented; a number of HCV-encoded T_(reg) cell epitopes derived from structural, as well as non-structural, HCV proteins have been reported. The invention described is the first to identify a promiscuous, HCV peptide sequence (HCV_G1_p7_(—)794) that exhibits extensive human homology and the ability to induce T_(reg) cells in vitro. HCV_G1_p7_(—)794 added to PBMCs cultures derived from HCV-infected patients, but not from non-infected individuals or patients who cleared infection, induced a marked increase in CD3⁺CD4⁺FoxP3⁺ cells. In addition to expressing CD25, characteristic of T_(reg) cells, the vast majority of these cells expressed CD39, a marker that distinguishes FoxP3⁺ T_(reg) cells from activated T_(eff) cells that transiently express FoxP3, but not suppressor activity.

In contrast to HCV_G1_p7_(—)794, the human peptide analog (p7_(—)794) elicited a significant increase in CD3⁺CD4⁺FoxP3⁺ cells in PBMC cultures derived from non-infected individuals with no evidence of prior HCV exposure, as well as HCV-infected patients. This finding is congruent with the suggestion that viral epitopes with human homology influence the pathogenesis of chronic HCV by activating preexisting, cross-reactive nT_(reg) cells. Indeed, extensive homology between the HCV polyprotein and proteins that comprise human proteome is well documented. JanusMatrix, a bioinformatics algorithm that interrogates potential T cell epitopes from both their HLA-binding and TcR-facing aspects, confirmed the existence of significant homology between HCV_G1_p7_(—)794 and hundreds of proteins that compose the human proteome. The results of this analysis demonstrate the potential efficacy of JanusMatrix in identifying pathogen-encoded epitopes that elicit the activity of nT_(reg) cells, which normally function to suppress autoimmune reactivity to self antigens (proteins). In this regard, it is pertinent to remark that HCV_G1_p7_(—)794 is comprised of epitopes that are homologous to those found in hundreds of human proteins. This suggests the autoimmune response to a large number of proteins is inhibited by a single or limited number of nT_(reg) cell clones responsive to a common peptide sequence, rather than a large number of clones each responsive to a unique sequence in each protein.

Although immunosuppression is a defining characteristic of T_(reg) cells and readily demonstrated in animal (mouse) models, demonstrating the suppressor activity of human CD3⁺CD4⁺CD25⁺FoxP3⁺ T_(reg) cells in vitro, however, has proven problematic. Thus, while HCV_G1_p7_(—)794 induced a 3- to 4-fold increase in CD3⁺CD4⁺CD25⁺FoxP3⁺ cells in PBMC cultures derived from HCV-infected patients in the studies reported here, these cells exerted only a limited effect on the nonspecific proliferative response of cells stimulated with anti-CD3. Recent studies indicate that the nature of the responder T cells (CD4⁺CD25⁻ versus CD4⁺CD25^(low)) and the ratio of purified T_(reg) cells to purified responder cells exert significant effects on the outcome of suppression assays. Notably, in the experiments reported here, HCV_G1_p7_(—)794 was added to heterogeneous PBMC cultures in which the CD3⁺CD4⁺FoxP3⁻ responder, far outnumbered the CD3⁺CD4⁺CD25⁺FoxP3⁺ suppressor, cells by >10:1. Importantly, the addition of HCV_G1_p7_(—)794 alone to PBMC cultures derived from HCV-infected (Ab⁺VL⁺) patients failed to induce cell proliferation despite a marked (3- to 4-fold) increase in CD3⁺CD4⁺CD25⁺FoxP3⁺ cell number. This finding suggests that HCV_G1_p7_(—)794 induces the conversion of conventional T_(eff) to T_(reg) cells, i.e., infectious tolerance, a suggestion supported by studies demonstrating the inability of nT_(reg) cells to proliferate in response to their cognate antigen in vitro. Furthermore, in contrast to Ab⁺VL⁺ PBMCs cultured in medium alone, only a minority of CD3⁺CD4⁺FoxP3⁺ cells derived from PBMCs cultured in the presence of HCV_G1_p7_(—)794 expressed CD304 (neuropilin), which is expressed by a subset of FoxP3⁺ T_(reg) cells in humans and associated specifically with nT_(reg) cells in mice. While it has been suggested alternatively that the expanded T_(reg) cell population in chronic, HCV infected patients is composed of cells phenotypically similar to nT_(reg) or iT_(reg) cells, our results concur with the consensus that the expanded T_(reg) cell population in chronic HCV-infected patients is heterogeneous, composed of both T_(reg) cell subsets.

Taken together, the findings showed that HCV non-structural protein p7 contains a unique peptide sequence (HCV_G1_p7_(—)794), which is recognized by the TcR repertoire expressed by nT_(reg) cells that function normally to suppress the autoimmune response to hundreds of human proteins. Upon HCV_G1_p7_(—)794 recognition, these nT_(reg) cells induce the conversion of conventional T_(eff) cells to iT_(reg) cells (i.e. infectious tolerance). It is expected that the nT_(reg) cells and iT_(reg) cells responsive to HCV_G1_p7_(—)794 contribute to the elevated T_(reg) cell population found in HCV-infected patients, and play a role in immunosuppression and viral persistence.

Those skilled in the art will appreciate that numerous modifications and variations may be made to the above disclosed embodiments and contained in the claims without departing from the spirit and scope of the present invention. 

What is claimed is:
 1. A pharmaceutical composition used to suppress immunity in an animal, wherein the pharmaceutical composition comprises an isolated T-cell epitope peptide containing an amino acid sequence of PLLLLLLXLPXRA (SEQ ID NO: 5), wherein X is an amino acid.
 2. The pharmaceutical composition of claim 1, wherein the PLLLLLLXLPXRA peptide (SEQ ID NO: 5) is selected from a group consisting of PLLLLLLSLPPRA (SEQ ID NO: 2) or PLLLLLLALQRA (SEQ ID NO: 6).
 3. The pharmaceutical composition of claim 1 and a pharmaceutically acceptable carrier.
 4. A method of suppressing an antigen-specific immune response to a target antigen in a subject comprising administering to the subject a therapeutically effective amount of a pharmaceutical composition comprising the T-cell epitope polypeptide of claim 1, wherein the T-cell epitope polypeptide is either covalently bound, non-covalently bound or in admixture with the target antigen resulting in the diminution of immune response against the target antigen.
 5. The method of claim 4, wherein the suppressive effect is mediated by a natural Treg.
 6. The method of claim 5, wherein the suppressive effect is mediated by viral homolog of the natural Treg.
 7. The method of claim 4, wherein the pharmaceutical composition suppresses T cell epitope polypeptide an effector T cell response.
 8. The method of claim 4, wherein the pharmaceutical composition suppresses T cell epitope polypeptide a helper T cell response.
 9. The method of claim 4, wherein the pharmaceutical composition suppresses T cell epitope polypeptide a B cell response.
 10. A method for enhancing the immunogenicity of a vaccine delivery vector containing a virus, comprising identification and removal of a regulatory T cell epitope residing in the virus, wherein the regulatory T cell epitope suppresses an antigen-specific immune response.
 11. The method of claim 10, wherein the vaccine delivery vector with removed regulatory T cell epitopes is further enhanced, further comprising (a) isolating regulatory T-cells from the biological sample; (b) contacting the isolated regulatory T-cells with an effective amount of the enhanced vaccine delivery vector; (c) increasing the numbers of regulatory T-cells; (d) identification of the T cell epitopes sequences; and (e) removal of remaining regulatory T cell epitopes residing in the vaccine.
 12. The method of claim 10, wherein the removed regulatory T cell epitope of the vaccine delivery vector is an isolated T-cell epitope peptide selected from a group consisting of PLLLLLLALQRA (SEQ ID NO: 6) or the human homolog amino acid sequence of PLLLLLLSLPPRA (SEQ ID NO: 2).
 13. The method of claim 10, wherein virus in the vaccine delivery vector is hepatitis C virus.
 14. A therapeutic antibody used to reduce immunosuppression or viral persistence in an animal infected with virus, wherein the therapeutic antibody comprising a peptide containing an amino acid sequence of PLLLLLLXLPXRA (SEQ ID NO: 5), wherein X is an amino acid.
 15. The therapeutic antibody of claim 14, wherein the PLLLLLLXLPXRA peptide (SEQ ID NO: 5) is selected from a group consisting of PLLLLLLSLPPRA (SEQ ID NO: 2) or PLLLLLLALQRA (SEQ ID NO: 6).
 16. The therapeutic antibody of claim 14, wherein virus in the vaccine delivery vector is hepatitis C virus. 